Meetings & Conferences

SBML Hackathon Day 2

Things changing with SBML Level 3

A complete list is available at

These are just the ones I found the most interesting as we went through the whole list.

+ Move species type and compartment type outside of the core. These were used for annotation reasons, but could also do it with the species and compartments using their annotation/RDF sections. If the reason to use it was to group together things for annotation, why just for species and compartments? Why not for all things? In which case, a generic mechanism would be a good thing. Further, the original reason for them was as the first step in a generalized reaction (e.g. automatically generate reactions when all matched species are present in the compartment). If they ever generalize reactions, then they will reintroduce something that works in a similar way as an extension. In summary, what these things do will be done within the new Annotation package that will be part of Level 3.
+ Remove default values on optional attributes and make the necessary adjustments.
+ Introduce an SIdRef/UnitSId type. These types will match the SId / UnitSId, and will allow differentiation between ids that are references and ids that are ids. This is a really good idea, and will help out with the Xpath-based referencing method used in the L3 hierarchical modelling extension.
+ Update the units section
+ Update the reactions section. This improves how stoichiometry is dealt with. Will explain reaction extent, add sections for stoichiometry and conversion factor and remove stoichiometryMath. You cannot show a distinction between targets for optimization and those which aren't. However, this isn't a problem that is strictly for SBML, as "parameter" in SBML means something different.
+ Remove the parts of the spec that belong in a Best Practices document
+ Remove the parts of the explanation of kinetics for multicompartment models

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot – just let me know!

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By Allyson Lister

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